====== NewHybrids ======
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**[[http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm|NewHybrids]]**\\
[[http://ib.berkeley.edu/labs/slatkin/eriq/software/new_hybs_doc1_1Beta3.pdf|manual]]


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NewHybrids version 1.1 beta (7. April 2003)\\
NewHybrids is a program for computing the posterior distribution that individuals in a sample fall into different hybrid categories.

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===== Program information =====
  * Mac
  * Windows
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===== Data type handled =====
  * diploid
  * AFLP
  * MICROSAT
  * Standard

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===== Input Files =====
  * whitespace (spaces and or tabs) separated text file *.txt/*.dat
  * first line: ''NumIndivs '' number of individuals
  * second line: ''NumLoci '' number of loci
  * third line: ''Digits '' number of digits used to denote a particular allele
  * fourth line: ''Format '' ''Lumped'' (genotype at a single locus is given by a single number) or ''NonLumped''
  * next lines: ''LocusNames'' names of all loci separated by whitespace 
  * next lines: genotype data
    * first character: number of the individual (numbering must be serially)
    * next characters: genotypes (all on same line or on different lines)
      * ''Lumped'' format: two alleles are encoded as one number, ''Digits'' specify how many digits are used to represent each locus
      * ''NonLumped'' format: alleles at each locus are given by a consecutive pair of numbers that are white space seperated
      * Missing data: ''Lumped'': encoded as ''0'', ''NonLumped'': encoded as ''-1'' (each allele at the missing locus must have a ''-1'')

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==== AFLP data ====
  * ''Lumped'' format
  * ''+'' band is present
  * ''-'' band is absent
  * ''0'' missing data

  * data types can be mixed

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==== Example ====
  * ''Lumped'' data file:
<code>
NumIndivs 2
NumLoci 6
Digits 1
Format Lumped
LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH
1 11 11 11 0 11 32
2 21 11 21 11 11 12 
</code>
  * ''NonLumped'' data file:
<code>
NumIndivs 2
NumLoci 6
Digits 1
Format NonLumped
LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH
1 123 143 -1 -1 144 144 120 122 157 158 144 144 
2 135 135 134 140 144 144 120 122 161 161 144 144 
</code>
  * AFLP data file (4 Microsat loci, 5 AFLP loci):
<code>
NumIndivs 2
NumLoci 9
Digits 1
Format Lumped
LocusNames m1 m2 m3 m4 A1 A2 A3 A4 A5
1 11 12 13 11 + + + - +
2 22 33 11 22 - - 0 - -
3 12 13 13 11 + - - - +
</code>

===== How to cite =====
Anderson, E.C. and Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217-1229.